{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "53cb155f",
   "metadata": {},
   "source": [
    "# Preparation of SpatialCOC"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9eb357bd",
   "metadata": {},
   "source": [
    "We recommend using a dedicated conda environment to run SpatialCOC. Please download and install Anaconda3 from the official website.\n",
    "> https://www.anaconda.com/download"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b288244b",
   "metadata": {},
   "source": "## 1. Install SpatialCOC"
  },
  {
   "cell_type": "markdown",
   "id": "bc6e53f5",
   "metadata": {},
   "source": "### 1.1 Create a conda environment"
  },
  {
   "cell_type": "markdown",
   "id": "5c5f0bb8",
   "metadata": {},
   "source": "Please execute the following commands in the Anaconda Prompt:"
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e84b9497",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create a new environment named SpatialCOC with Python 3.11.5\n",
    "conda create -n SpatialCOC python=3.11.5\n",
    "\n",
    "# Activate the environment\n",
    "conda activate SpatialCOC"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b771de8e",
   "metadata": {},
   "source": "### 1.2 Install the SpatialCOC package"
  },
  {
   "cell_type": "markdown",
   "id": "8c15183b",
   "metadata": {},
   "source": [
    "Download the SpatialCOC package from the GitHub repository.\n",
    "> https://github.com/xjtu-omics/SpatialCOC\n",
    "\n",
    "After downloading, navigate to the package directory and run the following command to install the package:"
   ]
  },
  {
   "cell_type": "code",
   "id": "5fe12a07",
   "metadata": {},
   "source": "pip install .",
   "outputs": [],
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "id": "f3472660",
   "metadata": {},
   "source": "Once the installation is complete, you can verify that SpatialCOC is imported successfully:"
  },
  {
   "cell_type": "code",
   "id": "7d411eec",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-01T06:22:06.369229200Z",
     "start_time": "2026-04-01T06:22:06.341752400Z"
    }
   },
   "source": [
    "try:\n",
    "    import SpatialCOC\n",
    "    print(\"✓ SpatialCOC imported successfully!\")\n",
    "    print(f\"  SpatialCOC version: {SpatialCOC.__version__}\")\n",
    "\n",
    "except ImportError as e:\n",
    "    print(f\"✗ Import failed: {e}\")\n",
    "    print(\"  Please install SpatialCOC: pip install SpatialCOC\")\n",
    "except Exception as e:\n",
    "    print(f\"✗ Other error: {e}\")"
   ],
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✓ SpatialCOC imported successfully!\n",
      "  SpatialCOC version: 1.0.0\n"
     ]
    }
   ],
   "execution_count": 12
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "## 2. Configure the R Environment",
   "id": "ccd7c809a822e96f"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "SpatialCOC uses the mclust algorithm, which requires both the rpy2 Python package and the mclust R package.",
   "id": "14dd1ce8ebb07d3d"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "### 2.1 Install the R software\n",
    "Download and install R version 4.3.1 to a specific directory.\n",
    "> https://cran.r-project.org/bin/windows/base/old/4.3.1/"
   ],
   "id": "e1b312f91b54ce78"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "### 2.2 Install the rpy2 package",
   "id": "4ff9a83cc9e8c391"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "Please run the code below to install the rpy2 package:",
   "id": "849ceb99bc9e7499"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "conda install -c conda-forge rpy2",
   "id": "fea324f8fe84b914"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "### 2.3 Set the correct paths",
   "id": "ce2d53e39f822441"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "To enable rpy2 to work properly, configure the following environment variables. Replace the placeholders with your actual paths:",
   "id": "c40f9fc2c105f668"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-01T06:22:56.777824700Z",
     "start_time": "2026-04-01T06:22:56.762719400Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import os\n",
    "os.environ['RPY2_CFFI_MODE'] = 'ABI'\n",
    "\n",
    "os.environ['R_HOME'] = '***'    # Path to the R installation, e.g., 'E:/R-4.3.1'\n",
    "os.environ['R_USER'] = '***'    # Path to rpy2 within the virtual environment, e.g., 'E:/anaconda3/envs/SpatialCOC/Lib/site-packages/rpy2'"
   ],
   "id": "de8a26c77b50d176",
   "outputs": [],
   "execution_count": 16
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "Please run the following code to confirm that rpy2 is correctly installed and can communicate with R:",
   "id": "b8219cf9a35e7789"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2026-04-01T06:22:58.939724600Z",
     "start_time": "2026-04-01T06:22:58.921308Z"
    }
   },
   "cell_type": "code",
   "source": [
    "try:\n",
    "    import rpy2.robjects as robjects\n",
    "    import rpy2.robjects.numpy2ri\n",
    "    print(\"✓ rpy2 imported successfully!\")\n",
    "    print(f\"  rpy2 version: {robjects.__version__}\")\n",
    "\n",
    "    # Get R version\n",
    "    r_version = robjects.r('R.version.string')[0]\n",
    "    print(f\"  R version: {r_version}\")\n",
    "\n",
    "except ImportError as e:\n",
    "    print(f\"✗ Import failed: {e}\")\n",
    "    print(\"  Please install rpy2: pip install rpy2\")\n",
    "except Exception as e:\n",
    "    print(f\"✗ Other error: {e}\")"
   ],
   "id": "a9dc4c768106f814",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "✓ rpy2 imported successfully!\n",
      "  rpy2 version: 3.6.3\n",
      "  R version: R version 4.3.1 (2023-06-16 ucrt)\n"
     ]
    }
   ],
   "execution_count": 17
  }
 ],
 "metadata": {
  "language_info": {
   "name": "python"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}